Removed a bunch of superflueous makefiles
Made simpler makefile in root.

PHYS-24 #time 3h #comment Still need to work out some kinks. Right now the .d and .o files are being created in the true src directory because I'm having issues getting an object to point to its corresponding source files otherwise.
Deleted a bunch of old files.

PHYS-24 #time 25m #comment Might regret doing this because I won't have old examples to use, but I think at this point I've successfully emulated the old behavior (Aside from the target directories for output files) so I'll mainly be focused on simplifying the new approach.
Trying to simplify further by looping directories

PHYS-24 #time 15m
Got rid of noisy output
Add first Catch unit tests

PHYS-25 #time 1h

There are some big obvious flaws in how I'm currently doing these, but I
just wanted to get started on tests.

I need to decide:
Where individual tests should be
How they should be compiled
Hierarchy of various test classes
Temporarily move unitTests out of the way

PHYS-25 #time 20m #comment I need to figure out the best way to compile
this class and link against the various objects it needs. After that,
hopefully I can start dividing them up in a logical manner.
Delete garbage subdir.mk files

PHYS-24 #time 25m
Generate .d files properly for cleaning

PHYS-24 #time 10m
Get rid of objects.mk. Remove old subdir references
Move all building into single makefile

PHYS-24 #time 25m

I think?? this is working, but the output is totally screwy right now.
From looking at the output, I would expect everything to be completely
broken, but somehow it works...
Continue removing bits from makefile

PHYS-24 #time 25m
Merge branch 'nightly' into PHYS-25
Verify that unit tests work with new makefile

PHYS-25 #time 15m
Add test for updating dimensions of Simulation

PHYS-25 #time 10m
Delete dumb .d file
Fix typo

PHYS-24 #time 5m
Merge branch 'nightly' into PHYS-24

Conflicts:
	Release/makefile
Make single root-level makefile behave correctly

PHYS-24 #time 45m
Minor makefile cleanup

PHYS-24 #time 5m